Studies of virus structure by laser-Raman spectroscopy. II. MS2 phage, MS2 capsids and MS2 RNA in aqueous solutions.

Laser-Raman spectra of the bacteriophage MS2, and of its isolated coat-protein and RNA components, have been obtained as a function of temperature in both H₂O and D₂O (deuterium oxide) solutions. The prominent Raman lines in the spectra are assigned to the amino acid residues and polypeptide backbone of the viral coat protein and to the nucleotide residues and ribosyl-phosphate backbone of the viral RNA. The Raman frequencies and intensities, and their temperature dependence, indicate the following features of MS2 structure and stability. Coat-protein molecules in the native phage maintain a conformation determined largely by regions of β-sheet (~60%) and random-chain (~40%) structures. There are no disulfide bridges in the virion and all sulfhydryl groups are accessible to solvent molecules. Protein-protein interactions in the virion are stable up to 50 °C. Release of viral RNA from the virion does not affect either the conformation of the coat-protein molecules or the thermal stability of the capsid. MS2 RNA within the virion contains a highly ordered secondary structure in which most (~85%) of the bases are either paired or stacked or both paired and stacked and in which the RNA backbone assumes a geometry of the A-type. When RNA is partially or fully released from the virion its overall secondary structure at 32 °C is unchanged. However, the exposed RNA is more susceptible to changes in secondary structure promoted by increasing the temperature. Thus the viral capsid exerts a significant stabilizing effect on the secondary structure of MS2 RNA. This stabilization is ionic-strength dependent, being more pronounced in solutions containing high concentrations of KCl. Raman intensity profiles as a function of temperature reveal that disordering of the MS2 RNA backbone and rupture of hydrogen-bonding between complementary bases are gradual processes, the major portions of which occur above 40 °C. However, the unstacking of purine and pyrimidine bases is a more co-operative phenomenon occurring almost exclusively above 55 °C.     

Preliminary results on the photoluminescence and optically stimulated luminescence in Cu‐doped and Ag‐doped ZnB2X4 (B = Li,Na, K: X = Cl,Br) compounds

Photoluminescence, and optically stimulated luminescence in ZnB₂X₄ (B; Li,Na,K: X; Cl,Br) compounds doped with Cu⁺ or Ag⁺ were studied. Double humped emission bands attributable to the activators were observed in all the samples. The observed photoluminescence of Cu⁺ and Ag⁺ could be identified with 3d⁹4s¹?3d¹⁰ and 4d⁹5s¹?5d¹⁰ transitions respectively. The longer wavelength band (400–500 nm range) could be attributed to the Cu⁺ or Ag⁺ ion replacing alkali ion at the octahedral alkali site whereas short wavelength band (340–400 nm range) is attributed to a Cu or Ag ion at tetrahedral zinc site. The short wavelength band was found to be intense compared with long wavelength and gave an indication that most of the Cu or Ag ions prefered a tetrahedral Zn site compared with the octahedral alkali site. All the samples exhibit optically stimulated luminescence (OSL). The sensitivity was found to be lattice dependent. The lowest sensitivity of about 1% compared with Al₂O₃:C was observed in lithium lattices whereas highest the sensitivity of about 290% was observed in the case of Cu‐doped ZnNa₂Br₄.     

Conformational flexibility and structural variability of SARS-CoV2 S protein

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Sol–gel synthesis and luminescence property of Sr4Al2O7:Re3+,R+ (Re = Eu and Dy; R = Li,Na and K) phosphors for white LEDs

Sr₄Al₂O₇:Eu³⁺ and Sr₄Al₂O₇:Dy³⁺ phosphors with alkali metal substitution were prepared using a sol–gel method. The effects of a charge compensator R on the structure and luminescence of Sr₄Al₂O₇:Re³⁺,R⁺ (Re = Eu and Dy; R = Li, Na and K) phosphors were investigated in detail. Upon heating to 1400°C, the structure of the prepared samples was that of the standard phase of Sr₄Al₂O₇. Under ultraviolet excitation, all Sr₄Al₂O₇:Eu³⁺,R⁺ samples exhibited several narrow emission peaks ranging from 550 to 700 nm due to the 4f → 4f transition of Eu³⁺ ions. All Sr₄Al₂O₇:Dy³⁺,R⁺ phosphors showed two emission peaks at 492 and 582 nm, due to the ⁴F_9/2 → ⁶H_15/2 and ⁴F_9/2 → ⁶H_13/2 transitions of Dy³⁺ ions, respectively. The luminescence intensity of Sr₄Al₂O₇:Re³⁺,R⁺ (Re = Eu and Dy; R = Li, Na and K) phosphors improved markedly upon the addition of charge compensators, promoting their application in white light‐emitting diodes with a near‐ultraviolet chip.     

Neoantigen-driven B cell and CD4 T follicular helper cell collaboration promotes anti-tumor CD8 T cell responses

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Synthesis and photoluminescence properties of red emitting phosphor La2–xEuxLi0.5Al0.5O4 [x = 0.2–2] with K2NiF4 structure

Europium (Eu)³⁺‐substituted La₂Li_0.5Al_0.5O₄ red emitting phosphors were prepared by a conventional high‐temperature solid‐state reaction method. Powder X‐ray diffraction, diffuse reflectance spectra and spectrofluorometry were used as vital characterizing tools for the phosphors. The Eu concentration dependence luminescence properties and Judd–Ofelt intensity parameters were investigated and calculated, respectively. All compositions showed an orange red emission (due to the magnetic and electric dipole transitions of the Eu³⁺ ion) with the appropriate Commission Internationale de l'Eclairage (CIE) colour gamut under near ultraviolet or blue ray light excitation. The calculated critical distance showed that the energy transfer occured between Eu to Eu via an exchange mechanism. The Eu_1.4La_0.6Li_0.5Al_0.5O₄ composition showed the highest red emission intensity with CIE colour saturation compared with that of the commercial Eu‐activated yttrium oxysulfide red phosphor.     

The structural definition of some novel adducts of stoichiometry CuX:dpex:MeCN (2:1:1)(n), X = (pseudo-) halogen,dppx = Ph2E(CH2)xEPh2, E = P,As, Sb

Single-crystal X-ray studies have defined the structures of a number of novel adducts of the form CuX:dpex (2:1), X = (pseudo-)halide, dpex = bis(diphenylpnicogeno)alkane, Ph₂E(CH₂)_xEPh₂, E = P, As, of diverse types, solvated with acetonitrile. CuBr:dpem (2:1)₂. 2MeCN (E = both P, As) are tetranuclear, derivative of the familiar ‘step’ structure, while CuCl:dpph (MeCN solvate) and CuBr:dppe (MeCN solvate) yield one-dimensional polymers (i.e., x = 1, 2, 6 for dppx, x = m, e, h), as also does CuSCN:dpam (MeCN solvate). In CuI:dpsm:MeCN (3:1:2) (‘dpsm’ = Ph₂Sb(CH₂)SbPh₂), CuI:dpsm (2:1)₂ ‘step’ units are connected into an infinite ‘stair’ polymer by interspersed (MeCN)CuI linkers.     

RGD序列修饰的MS2噬菌体样颗粒的构建及表达

目的:构建并表达衣壳蛋白表面展示有精氨酸-甘氨酸-天冬氨酸(RGD)序列的MS2噬菌体样颗粒,以期获得肿瘤细胞靶向性RNA递送载体。方法:用分子克隆技术将RGD4C编码序列插入MS2衣壳蛋白编码基因,然后构建到p ETDuet-1质粒多克隆位点MCS1上;将含有MS2噬菌体包装位点的pre-let-7编码基因构建到p ETDuet-1质粒多克隆位点MCS2上;重组质粒转化大肠杆菌,表达产物纯化后经琼脂糖凝胶电泳、电子显微镜鉴定。结果和结论:采用分子克隆技术和原核细胞单质粒双表达系统获得表面展示有RGD序列,内部包装有pre-let-7 RNA的MS2噬菌体样颗粒,为体内和体外研究其肿瘤细胞靶向递送和功能奠定了基础。     

Photoluminescent properties of Eu3+‐Eu2+ activated MAl2SixO2x + 4 (M = Mg,Ca, Sr,Ba) phosphors prepared in air

In this paper, MAl₂Si_xO_2x+4:Eu²⁺/Eu³⁺ (Eu²⁺ + Eu³⁺ = 2%, molar ratio; M = Mg, Ca, Sr, Ba; x = 0, 0.5, 1, 1.5, 2) phosphors with different SiO₂ concentrations (the ratio of SiO₂ to MAl₂O₄ is n%, n = 0, 50, 100, 150, 200, respectively) were prepared by high‐temperature solid‐state reaction under atmospheric air conditions. Their structures and photoluminescent properties were systematically researched. The results indicate that Eu³⁺ ions have been reduced and Eu²⁺ ions are obtained in air through the self‐reduction mechanism. The alkaline earth metal ions and doping SiO₂ strongly affect the crystalline phase and photoluminescent properties of samples, including microstructures, relative intensity of Eu²⁺ to Eu³⁺, location of emission lines/bands. It is interesting and important that the emission color and intensities of europium‐doped various phosphors which consist of aluminosilicate matrices prepared under atmospheric air conditions could be modulated by changing the kinds of alkaline earth metal and the content of SiO₂.     

Bacteriophage T4 gp2 Interferes with Cell Viability and with Bacteriophage Lambda Red Recombination

The T4 head protein, gp2, promotes head-tail joining during phage morphogenesis and is also incorporated into the phage head. It protects the injected DNA from degradation by exonuclease V during the subsequent infection. In this study, we show that recombinant gp2, a very basic protein, rapidly kills the cells in which it is expressed. To further illustrate the protectiveness of gp2 for DNA termini, we compare the effect of gp2 expression on Red-mediated and Int-mediated recombination. Red-mediated recombination is nonspecific and requires the transient formation of double-stranded DNA termini. Int-mediated recombination, on the other hand, is site specific and does not require chromosomal termini. Red-mediated recombination is inhibited to a much greater extent than is Int-mediated recombination. We conclude from the results of these physiological and genetic experiments that T4 gp2 expression, like Mu Gam expression, kills bacteria by binding to double-stranded DNA termini, the most likely mode for its protection of entering phage DNA from exonuclease V.     

Synthesis and solution behavior of the trinuclear palladium(II) unsaturated carboxylate complexes triangle-Pd3[μ-O2CC(R′) = CHMe]6 (R′ = Me, H): X-ray structure of palladium(II) tiglate (R′ = Me)

The first examples of binary palladium(II) derivatives of unsaturated carboxylic acids are reported. It was found that the interaction of Pd₃(μ-OAc)₆ with the ,β-unsaturated 1-methylcrotonic (tiglic) and crotonic acids leads to the corresponding carboxylates of composition Pd₃[μ-O₂CC(R′) = CHMe]₆, where R′ = Me (1) or H (2). The new compounds have been characterized by elemental analysis, solid and solution IR, ¹H and ¹³C NMR, and ESI mass spectrometry. The crystal structure of 1 has been determined. This molecule displays a central Pd₃ cyclic core with Pd–Pd distances of 3.093–3.171 Å. Each Pd–Pd bond is bridged by a pair of carboxylate ligands, one above and the other below the Pd₃ plane, providing a square planar coordination for each Pd atom in an approximate D_3h overall symmetry arrangement. Solution spectroscopic data show that the bridging η¹:η¹:μ₂ interaction of the carboxylates of 1 and 2 is readily displaced, with a change of the ligand to the terminal (η¹) coordination mode.     

Hydrothermal synthesis and crystal structure of [Co(2,5-pydc)(H2O)2]n · nH2O (2,5-pydc = 2,5-pyridinedicarboxylate)

A new cobalt(II) compound, [Co(2,5-pydc)(H₂O)₂]_n · nH₂O (1) has been synthesized hydrothermally and characterized by elemental analysis, infrared spectroscopy, thermogravimetric analysis, and single crystal X-ray diffraction. The crystal structure consists of Co(II) centers linked via 2,5-pydc ligands and water molecules, in which every 2,5-pydc ligand adopts the coordination form in quadridentate –NOOO′ mode. The structure is 2-D networks and neighboring layers are further extended into a 3-D supramolecular architecture through hydrogen-bonding interactions between water molecules and carboxyl oxygen atoms.     

Isostructural M(RL)2(hfac)2 complexes with RL = 5-(4-[N-tert-butyl-N-aminoxyl]phenyl)pyrimidine

5-(4-(N-tert-Butyl-N-aminoxylphenyl))pyrimidine (RL, 4PPN) forms crystallographically isostructural and isomorphic pseudo-octahedral M(RL)₂(hfac)₂ complexes with M(hfac)₂, M = Zn, Cu, Ni, Co, and Mn. Multiple close contacts occur between sites of significant spin density of the organic radical units. Magnetic behavior of the Zn, Cu, Ni, Co complexes appears to involve multiple exchange pathways, with multiple close crystallographic contacts between sites that EPR (of 4PPN) indicates to have observable spin density. Powder EPR spectra at room temperature and low temperature are reported for each complex. Near room temperature, the magnetic moments of the complexes are roughly equal to those expected by a sum of non-interacting moments (two radicals plus ion). As temperature decreases, AFM exchange interactions become evident in all of the complexes. The closest fits to the magnetic data were found for a 1-D Heisenberg AFM chain model in the Zn(II) complex (J/k = (?)7 K), and for three-spin RL—M—RL exchange in the other complexes (J/k = (?)26 K, (?)3 K, (?)6 K, for Cu(II), Ni(II), and Co(II) complexes, respectively).     

Resonant and non‐resonant energy transfer from Ce3+ → X (X = Tb3+, Eu3+ or Dy3+) in NaMgSO4F material

An inorganic NaMgSO₄F fluoride material was prepared by the wet chemical method and studied for its photoluminescence (PL) and resonant–non‐resonant energy transfer (RET and NORET) capabilities between Ce³⁺ → Tb³⁺, Ce³⁺ → Eu³⁺ and Ce³⁺ → Dy³⁺ rare earth ions. The Tb³⁺ emission for Ce³⁺ → Tb³⁺ transfers under ultraviolet (UV) wavelengths peaked at 491, 547, and 586 nm, for excitation at 308 nm due to ⁵D₄ → ⁷F_J (J = 4, 5, 6) transitions. Eu emission spectra were observed at 440 nm (Eu²⁺), 593 nm and 616 nm (Eu³⁺) recorded for different concentrations of materials, whereas Dy³⁺ emission from Ce³⁺ → Dy³⁺ transfer under UV wavelengths peaked at 485 nm and 577 nm due to ⁴F_9/2 → ⁶H_15/2 and ⁶H_13/2 transitions. The purpose of the present study is to understand the RET and NORET effects of Tb³⁺, Eu³⁺ and Dy³⁺ co‐doping in a NaMgSO₄F:Ce³⁺ luminescent material, which could be used as a green‐emitting material for lamp phosphors.     

Novel cell subtypes of SPP1 + S100P+, MS4A1-SPP1 + S100P+ were key subpopulations in intrahepatic cholangiocarcinoma

BackgroundIn this study, we integrated single-cell RNA sequencing (scRNA-seq) data to investigate cell heterogeneity and utilized MSigDB and CIBERSORTx to explore the pathways of major cell types and the relationships between different cell subtypes. Subsequently, we explored the correlation of cell subtypes with survival and used Gene Set Enrichment Analysis (GSEA) analyses to assess the pathways associated with the infiltration of specific cell subtypes. Finally, multiplex immunohistochemistry in tissue microarray cohort were performed to validate differences in protein level and their correlation with survival.ResultsiCCA presented a unique immune ecosystem, with increased proportions of Epi (epithelial)-SPP1–2, Epi-S100P-1, Epi-DN (double negative for SPP1 and S100P expression)-1, Epi-DN-2, Epi-DP (double positive for SPP1 and S100P expression)-1, Plasma B-3, Plasma B-2, B-HSPA1A-1, B-HSPA1A-2 cells, and decreased proportions of B-MS4A1. High level of Epi-DN-2, Epi-SPP1–1, Epi-SPP1–2, B-MS4A1, and low level of Epi-DB-1, Epi-S100P-1, and Epi-S100P-2 was significantly associated with longer overall survival (OS), and high level of B-MS4A1_Low_Epi-DN-2_Low was associated with the shortest OS. Moreover, the results of MsigDB and GSEA suggest that bile acid metabolism is a crucial process in iCCA. Finally, we found that S100P+, SPP1+, SPP1 + S100P+, and MS4A1-SPP1 + S100P+ were highly expressed, whereas MS4A1 was lowly expressed in iCCA, and patients with high level of S100P+, SPP1 + S100P+, and MS4A1-SPP1 + S100P+ exhibited shorter survival.ConclusionsWe identified the cell heterogeneity of iCCA, found that iCCA is a unique immune ecosystem with many cell subtypes, and showed that the novel cell subtypes of SPP1 + S100P+ and MS4A1-SPP1 + S100P+ were key subpopulations in iCCA.     

Non-Continuous Translation of Coat Protein and Ribonucleic Acid Polymerase Cistrons in MS2 Bacteriophage Ribonucleic Acid

In an MS2 phage ribonucleic acid (RNA)-directed in vitro protein-synthesizing system, the coat protein cistron and the adjacent RNA polymerase cistron are translated non-continuously. The ribosomes which have completed the synthesis of coat protein dissociate from the MS2 RNA and do not read through the intercistronic gap. Translation of the adjacent RNA polymerase cistron requires ribosomes other than those translating the coat protein cistron.     

Structure-guided T cell vaccine design for SARS-CoV-2 variants and sarbecoviruses

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